Detection of linkage
Mapping with molecular markers
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Alleles used as experimental probes to keep track of
an individual, a tissue, a cell, a nucleus, a chromosome,
or a gene are called markers.
In the first 70 years of building genetic maps these
markers with detectible phenotype were used.
However, even in those organisms in which the maps
appeared to be “full” of loci of known phenotypic
effect, measurements showed that the chromosomal
intervals between genes had to contain vast amounts
of DNA.
These gaps could not be mapped by linkage analysis,
because there were no markers in those regions.
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So, additional genetic markers were needed, that could
be used to fill in the gaps to provide a higher-resolution
map.
Ultimately molecular markers were discovered.
A molecular marker is a site of heterozygosity for
some type of silent DNA variation not associated with
any measurable phenotypic variation.
Such a “DNA locus,” when heterozygous, can be used in
mapping analysis.
Because molecular markers can be easily detected and
are so numerous in a genome, when they are mapped by
linkage analysis, they fill the voids between genes of
known phenotype.
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In this way, markers are being used just as milestones
were used by travelers in previous centuries.
Travelers were not interested in the milestones
(markers) themselves, but they would have been
disoriented without them.
The two basic types of molecular markers are those
based on restriction-site variation and on repetitive
DNA.
Gene Mutations
Lecture 6
Dr. Attya Bhatti
Any variation in the DNA sequence is called Mutation.
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In gene mutation, an allele of a gene changes, becoming a
different allele.
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As change takes place within a single gene is also called a
point mutation.
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To consider change, we must have a fixed reference point,
or standard.
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In genetics the wild type provides the standard.
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Any change away from the wild-type allele is called
forward mutation.
Any change back to the wild-type allele is called
reverse mutation (or reversion or back mutation).
For example,
The frequency of mutants in a population is called
mutation frequency.
At DNA level mutations are of following types
Base substitutions
Transitions
Transversions
Base additions or deletions
Silent substitution
Nonsense mutation
Missense mutation
Gene Mutations at the Molecular Level
Synonymous substitution:
It is substitution of a chemically similar amino acid and it
will have a less severe effect on the protein’s
structure and function.
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Nonsynonymous substitutions:
It is substitution of chemically different amino acid and
is more likely to produce severe changes in protein
structure and function.
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Mutations that are in or close to the active site of a
protein will most likely lead to lack of function; such
mutations are called null (nothing) mutations.
Mutations in less crucial areas of a protein will most
likely have less deleterious effect, often resulting in
“leaky,” or partly inactivated, mutants.
The effect of some common types of
mutations at the RNA and protein levels
Somatic versus germinal mutation
Mutant Types:
Morphological mutations
They affect the visible properties of an organism,
such as shape, color, or size.
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For Example;
Curly wings in Drosophila, and dwarf peas
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Lethal mutations
Lethal mutation affect the survival of the organism.
Mutant Types:
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Conditional mutations:
In the class of conditional mutations, a mutant allele
causes a mutant phenotype in only a certain
environment, called the restrictive condition, but
causes a wild-type phenotype in some different
environment, called the permissive condition.
For example,
certain Drosophila mutations are known as dominant
heat-sensitive lethals. Heterozygotes (say, H +/H) are
wild type at 20°C (the permissive condition) but die if
the temperature is raised to 30°C (the restrictive
condition).
Mutant Types:
Biochemical mutations:
They are charachterized by the loss or change of
some biochemical function of the cells.
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This change typically results in an inability to grow
and proliferate.
For example,
one class of biochemically mutant fungi will not grow unless
supplied with the nitrogenous base adenine.
Mutant Types:
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Loss-of-function mutations
Generally, loss-of-function
found to be recessive.
However, some
dominant.
(null)
mutations
are
loss-of-function
mutations
are
In such cases, the single wild-type allele in the
heterozygote cannot provide the amount of gene
product needed for the cells and the organism to
be wild type.
Mutant Types:
•(a)Mutation m has completely lost its
function (it is a null mutation).
•In the heterozygote, wild-type gene
product is still being made, and often
the amount is enough to result in a
wild-type phenotype, in which case, m
will act as a recessive.
•If the wild-type gene product is
insufficient, the mutation will be seen
as dominant.
•(b) Mutation m′ still retains some
function, but in the homozygote there
is not enough to produce a wild-type
phenotype.
•(c) Mutation M has acquired a new
cellular function represented by the
gene product colored green. M will be
expressed in the heterozygote and
most likely will act as a dominant. The
homozygous mutant may or may not
be viable, depending on the role of
the + allele.
Mutant Types:
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Gain-of-function mutations
Mutation which will produce a new function is called
gain of function mutation.
In a heterozygote, the new function will be
expressed, and therefore the gain-of-function
mutation most likely will act like a dominant allele
and produce some kind of new phenotype.
Mutation and cancer
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Cancer is a genetic disease.
Cancer has many causes, but ultimately all
these causes exert their effects on a
special class of genes called cancer genes
or proto-oncogenes.
Human chromosomes showing bands from Giemsa staining
and the positions (shown by black dots) of known protooncogenes; mutations in proto-oncogenes lead to cancer.
Comparison of the various outcomes of somatic
mutations in proto-oncogenes and other genes.